Bake action with euler rotation instead of quaternion
I found a workaround or temporal fix. In Blender version 2.92 (at this moment alpha version) the euler discontinuity filter has been improved. If you select the problematic bone, which has a flickering rotation after baking the action with euler rotation, you go into the Graph Editor -&gt; Key -&gt; Discontinuity Filter (Euler) at the top. At the moment, it fixes many of the rotation flickering but not all of them. Maybe in the future, it will fix all of the problematic keyframes, as it is still alpha.
Maybe this also helps other people with the same issue.